{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS2679CCWQ/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS2679CCWQ",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF1-BinA-PCR1-Rep1_S241",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF1-BinA-PCR2-Rep1_S247",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF1-BinA-PCR3-Rep1_S283",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF1-BinA-PCR4-Rep1_S289"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS2679CCWQ](/auxiliary-sets/IGVFDS2679CCWQ/) has sequence file(s) [IGVFFI3418LEES](/sequence-files/IGVFFI3418LEES/), [IGVFFI6704MRXG](/sequence-files/IGVFFI6704MRXG/), [IGVFFI9315FBJQ](/sequence-files/IGVFFI9315FBJQ/), [IGVFFI7466IBWF](/sequence-files/IGVFFI7466IBWF/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS2679CCWQ/"
}
]
},
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/6c75dbfa-635e-4a7a-8ec8-9e51e9c380a4/",
"title": "Jesse Engreitz"
},
"title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
},
"control_for": [],
"creation_timestamp": "2024-05-13T22:50:42.824103+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"accession": "IGVFDO0384OZRW",
"aliases": [
"igvf:donor_of_HCT116"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "gRNA sequencing",
"files": [
{
"@id": "/sequence-files/IGVFFI3418LEES/",
"accession": "IGVFFI3418LEES",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF1-BinA-PCR1-Rep1_S241"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:42:00.745300+00:00",
"file_format": "fastq",
"file_size": 17475784,
"href": "/sequence-files/IGVFFI3418LEES/@@download/IGVFFI3418LEES.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/b90fce61-0cb0-4404-bdf5-8134a4170a0c/IGVFFI3418LEES.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin6hrs-FF1-BinA-PCR1-Rep1_S241_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9209OTHM/",
"accession": "IGVFFI9209OTHM",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF1-BinA-PCR1-Rep1_S241"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:29:52.185880+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI9209OTHM/@@download/IGVFFI9209OTHM.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/95b92c12-268a-475b-b2f8-6361af82156a/IGVFFI9209OTHM.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF1-BinA-PCR1-Rep1_S241.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6704MRXG/",
"accession": "IGVFFI6704MRXG",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF1-BinA-PCR2-Rep1_S247"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:42:18.627982+00:00",
"file_format": "fastq",
"file_size": 19782959,
"href": "/sequence-files/IGVFFI6704MRXG/@@download/IGVFFI6704MRXG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/74f98fb8-a9be-4730-bd83-11a0be1ac0d2/IGVFFI6704MRXG.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin6hrs-FF1-BinA-PCR2-Rep1_S247_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9315FBJQ/",
"accession": "IGVFFI9315FBJQ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF1-BinA-PCR3-Rep1_S283"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:42:35.398421+00:00",
"file_format": "fastq",
"file_size": 25777163,
"href": "/sequence-files/IGVFFI9315FBJQ/@@download/IGVFFI9315FBJQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/adf31518-d9bc-49ac-8ab7-0c81bdb1bb46/IGVFFI9315FBJQ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin6hrs-FF1-BinA-PCR3-Rep1_S283_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7466IBWF/",
"accession": "IGVFFI7466IBWF",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_CCND1_Auxin6hrs-FF1-BinA-PCR4-Rep1_S289"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T01:42:53.176793+00:00",
"file_format": "fastq",
"file_size": 24849903,
"href": "/sequence-files/IGVFFI7466IBWF/@@download/IGVFFI7466IBWF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/6018e596-76df-48f3-ba6e-9f921e185c34/IGVFFI7466IBWF.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/CCND1-Auxin6hrs-FF1-BinA-PCR4-Rep1_S289_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1654NNBY/",
"accession": "IGVFFI1654NNBY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF1-BinA-PCR2-Rep1_S247"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:30:06.363110+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI1654NNBY/@@download/IGVFFI1654NNBY.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/b98bdce0-5c6b-457f-a9a5-9482c58ad9c5/IGVFFI1654NNBY.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF1-BinA-PCR2-Rep1_S247.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9506MMIO/",
"accession": "IGVFFI9506MMIO",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF1-BinA-PCR3-Rep1_S283"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:30:20.141074+00:00",
"file_format": "yaml",
"file_size": 915,
"href": "/configuration-files/IGVFFI9506MMIO/@@download/IGVFFI9506MMIO.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/15fc9198-164a-4399-bafd-01a772219871/IGVFFI9506MMIO.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF1-BinA-PCR3-Rep1_S283.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9345NUCS/",
"accession": "IGVFFI9345NUCS",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_CCND1_Auxin6hrs-FF1-BinA-PCR4-Rep1_S289"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:30:34.409270+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI9345NUCS/@@download/IGVFFI9345NUCS.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/05211eb1-3576-403f-bd38-a0e698a476e5/IGVFFI9345NUCS.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.CCND1_Auxin6hrs-FF1-BinA-PCR4-Rep1_S289.yaml",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS1569RNPD/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS0536HSAY/",
"accession": "IGVFDS0536HSAY",
"aliases": [
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF1-BinA-PCR1-Rep1_S241",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF1-BinA-PCR2-Rep1_S247",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF1-BinA-PCR3-Rep1_S283",
"jesse-engreitz:measurement_CRUDO_CCND1_Auxin6hrs-FF1-BinA-PCR4-Rep1_S289"
],
"preferred_assay_title": "CRISPR FlowFISH screen",
"status": "released"
}
],
"release_timestamp": "2024-07-10T20:09:11.348218+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0268CCRR/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0268CCRR",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF1-BinA-PCR1-Rep1_S241",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF1-BinA-PCR2-Rep1_S247",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF1-BinA-PCR3-Rep1_S283",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin6hrs-FF1-BinA-PCR4-Rep1_S289"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS6351FGNG/"
],
"modifications": [
{
"@id": "/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
"modality": "degradation",
"status": "released"
},
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002824/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:HCT116"
],
"status": "released",
"summary": "HCT116",
"term_name": "HCT116"
}
],
"status": "released",
"summary": "HCT116 cell line, male, Homo sapiens (sorting details: FACS bin A for 0-10% expression of CCND1) treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with AID system targeting RAD21, CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/",
"status": "released",
"treatment_term_name": "5-Phenyl-1H-indole-3-acetic acid"
}
]
}
],
"schema_version": "12",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-01T01:42:00.745300+00:00",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "391eb11a-4574-4273-848f-96c7dc044706"
}